chr4-28768220-G-T

Variant names:

• chr4-28768220-G-T
• rs7664880

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.293 in 151,420 control chromosomes in the GnomAD database, including 6,672 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6672 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44371 AN: 151302 Hom.: 6672 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.287

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.293 AC: 44371 AN: 151420 Hom.: 6672 Cov.: 31 AF XY: 0.293 AC XY: 21666 AN XY: 73998

African (AFR) AF: 0.243 AC: 10060 AN: 41324

American (AMR) AF: 0.308 AC: 4687 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3460

East Asian (EAS) AF: 0.169 AC: 866 AN: 5128

South Asian (SAS) AF: 0.258 AC: 1235 AN: 4796

European-Finnish (FIN) AF: 0.364 AC: 3818 AN: 10492

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22055 AN: 67726

Other (OTH) AF: 0.285 AC: 597 AN: 2096

Alfa AF: 0.312 Hom.: 30544

Bravo AF: 0.284

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.51
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7664880; hg19: chr4-28769842;